I think while migrating(by creating list  templates with or without data) list with some look-up fields or bdc columns  will loss the columns and this seems to be a common problem. I think instead of creating the List template  you create  a List Definition as like site definition. Or else export that List through stsadm.exe utility (this will be crude way to do and I cant assure the exact end results).

Regarding the content  Migration tool  failure in case of BDC data: I think the technical reason is, BDC pulls data  from external LOB which is not-all known to SharePoint. In that the data pulled-up is in readonly fashion. Thus even if the migration tool is actually pushing the same data into the bdc column, the column  will allow it (blame it to readonly nature) it will fail  to do so.

Let me know your thoughts on this.